Foodborne Illnesses / E. coli /

How is E. coli Infection Diagnosed?

How is Shiga toxin-producing E. coli (STEC) infection diagnosed?

Infection with E. coli O157:H7 or other STEC is almost always diagnosed by laboratory testing of a stool specimen from an ill individual. The lab test is typically ordered by a health care provider and tested at a clinical laboratory.

For many years, the only test was a stool culture, a type of test that could readily detect E. coli O157:H7 because its unique growth characteristics could be used to differentiate it from most other types of E. coli, including the many harmless strains that commonly inhabit the human intestine. Conversely, stool cultures cannot differentiate non-O157 STEC from the harmless E. coli and, thus, were not a useful diagnostic tool for them; this is why non-O157 STEC were so under-recognized as a cause of human illness for so long.

Then, in the late 1990s, tests for Shiga toxin itself were developed, and their use by clinical laboratories increased rapidly during the first decade of the 2000s. Because the detection of Shiga toxin is independent of whether the STEC serotype is O157 or non-O157, non-O157 STEC became increasingly identified. When a stool sample is positive for Shiga toxin, generally, an antigen test is done at the clinical lab to see if the STEC serotype is O157. If not, by definition the strain is usually a non-O157 serotype.

In the past few years, newer types of stool tests have been developed and are being used with greater frequency – these are called multiplex polymerase chain reaction (PCR) gastrointestinal syndrome panels. It is a complicated name, but it means that a single test can be used to test for multiple pathogens – up to 22 – at once, and it only takes an hour or two to complete. Shiga toxins, and sometimes also E. coli O157:H7, are specifically included in these tests.

National guidelines recommend that when STEC is a possible cause of illness, a stool sample should both be tested for Shiga toxin (to detect non-O157 STEC or O157) and cultured specifically for E. coli O157:H7. When people are diagnosed with a STEC infection, frequent monitoring of hemoglobin, platelet counts, electrolytes, and indicators of kidney function is recommended to detect early signs of HUS so that appropriate treatment can occur.

When a patient tests positive for any type of STEC, an isolate of the bacteria or the positive sample itself is often sent to the state public health lab for confirmation, determination of the serotype, and DNA fingerprinting. With the advent of whole genome sequencing, the serotype can be determined from the sequence.

Traceback and Source Identification of Human Shiga Toxin-producing E. coli (STEC) infections

When people are diagnosed with STEC through a laboratory test ordered by their health care provider, they become a “case” that is reported to their local or state public health department. Cases are interviewed by public health staff about possible sources for their infection (i.e., food, water, animal contact, ill people). In addition, the stool sample that tested positive, or the bacteria itself (called an “isolate”), is sent to the public health laboratory for confirmation and serotyping (to determine whether it is O157, O111, O26, etc.). Furthermore the STEC strain that is recovered undergoes molecular subtyping (DNA fingerprinting) to group cases together – cases that occur around the same time and have the same DNA fingerprint of O157, for example, are more likely to have acquired their infection from a common source and represent an outbreak due to that source. Therefore, public health staff compare the interviews of cases with the same STEC DNA fingerprint to try to determine what that common source is, solve the outbreak, and prevent further transmission. If you do have a STEC infection, it is in your best interest and that of your community to be as cooperative as you can with public health investigators and provide the best, most detailed information you can. This will help them determine the source of any outbreak that might be occurring.

Historically, pulsed-field gel electrophoresis (PFGE) has been the primary way of DNA fingerprinting STEC to identify and investigate outbreaks. In the wake of the 1992-93 Jack in the Box outbreak, in 1996, the Centers for Disease Control and Prevention (CDC) founded PulseNet, a national laboratory network that connects foodborne illness cases to detect outbreaks. PulseNet uses DNA fingerprinting of bacteria making people sick to detect thousands of local and multistate outbreaks around the United States. Through this network, state public health laboratories and other collaborators share PFGE results of STEC and other bacterial pathogens to better identify widespread outbreaks ( Another molecular subtyping technique called multiple locus variable number tandem repeat analysis (MLVA) has also been used to determine precise classification when it is difficult to differentiate between isolates with common PFGE patterns (

PFGE and PulseNet revolutionized foodborne disease surveillance by greatly enhancing detection and investigation of outbreaks. Smaller outbreaks were identified more frequently and more quickly. Large outbreaks were identified and controlled more quickly. Finally, the number of identified multi-state outbreaks due to widely distributed food products increased markedly.

As transformative as PFGE proved to be as a bacterial DNA fingerprinting tool, in 2019, it began to be replaced as the routine molecular subtyping method for STEC and other bacterial pathogens by whole genome sequencing, a method that is even more precise and effective (

Once a group of STEC cases with the same DNA fingerprint of STEC cases is identified, public health staff compare interviews of these cases and initiate further investigation (with local, state, and federal epidemiology, laboratory, environmental health/regulatory partners) to identify the outbreak vehicle and the mechanism for contamination (

It should be noted that over 80% of people with O157 (and more for non-O157 STEC) are never linked to an identified outbreak; for these people, called “sporadic” cases, the source of infection is very difficult to determine with any level of certainty. Identifying the source of infection would usually require attempts to isolate STEC from suspected food or animal sources and determine if isolates have the same DNA fingerprint as the human isolate; in practice, this is rarely done for single cases.